Smallville: A New Beginning S2EP1 Puppeteer
by NatDuv
Summary: After his nightmarish hallucination, Conner begins transforming. Lex realizes Other Lex is not a figment of his imagination.


**Smallville: A New Beginning**

**Season 2, Episode 1: Puppeteer**

Conner lifted up the fresh wooden beam off of the hey covered floors in the barn. He fixed the beam onto the area he marked for it and placed it down. He shoved it into the dirt beneath the space and pushed it down until it was deep into the ground.

"You're doing a great job with the barn, Conner." Clark said as he stepped in.

"I figured it would be better if I repaired the barn before she got back." Conner admitted.

"I was going to drive her back home from the hospital."

"You can't fly her back?"

"She just spent three weeks recovering in a hospital bed, it would be best if she took things slow from now on."

"Oh." Conner said, unenthusiastically.

"You could join me if you want."

"No, I think I'll stay here, finish the barn."

Clark sighed.

"Conner, what happened to her wasn't your fault."

"Then who's was it, Clark!"

"Conner it was a breach of trust, something like that could have happened to anyone."

"But I'm not just anyone. I can't afford to make those kinds of mistakes."

"Well blaming yourself doesn't change a thing."

"Then tell me how I can change this Clark!" Conner said.

"Be there for Ma, help her recover. Let her know she has help. You can't stop what happened from happening, but you can make sure things get better. Now I'm going to go to the Hospital and get her, we'll be back in an hour."

Conner nodded to Clark, who exited the barn for his car. When he saw Clark was gone he reached into his pocket, and felt for his phone. He pulled it out and speed-dialed a number.

"We need to meet up, if I can't stop it, the world may be in danger."

"Okay" The voice on the other end said. "Meet me in the Tower."

Conner ended the call and sped off.

* * *

Lena gathered her notepad from her bag and stuffed her bag in her locker. The students in the busy hallway, who walked past her, all said the same thing.

"Congratulations Lena."

"Good job."

"You did great."

She smiled, and closed her locker. She was startled as she saw a young man with dark hair there. He had a shifty look on his face, peach fuzz, and he smelled of cigarettes.

"Hi." She said, nervously.

"By any chance, is your name Lena Luthor?"

"Well, yes, it is."

"So you're the reason Cassie's in jail." He said. "Don't know if you realize this but, when you busted her you busted several others, now the police are on our backs. They're following a little trail of bread crumbs all our guys have left behind."

"Well that's good. Cassie was my friend and those drugs you guys had been using messing her up."

"No it's not good. You see, my supplier is a very rich man, and now that the drug trade is busted not only did you cost him millions, but now you've set a trail for the Feds to link to him. He doesn't like that."

"So what's he going to do about it?"

"If, he gets caught he'll lose everything, and so will you. Now he suggest, if you want your friends to be safe, your print a retraction, make a confession, take the fall. Unless you want Zoe and her family to be disposed of. You see, my boss, knows everything about you, he's told me everything. I know all your secrets, even the biggest one."

Lena looked startled as she heard his words.

"Watch yourself kid, because we are."

* * *

Lex sat in his private cabin in his Jet as it flew over the coast of Kaznia.

_"1 hour in Kaznia and you make an arms deal that practically gave you dominion over the Kaznian military."_

"A man with a clear objective can accomplish these kinds of things."

_"Impressive."_

"The Prometheus armor is a weapon like no other."

_"And might I say, you brilliantly executed Project 33.2"_

"Thanks, I found some of the records from my past life, each facility was destroyed by a terrorist group led by Oliver Queen, but how can the Green Arrow stop my plans if I'm not involved."

_"So you spread Kryptonite drugs throughout Smallville, in order to slowly create an army."_

"All under my control, the drugs make them violent, and then it messed with their minds, it reprograms them subliminally, until in the end, they follow me, and only me. Now, what bothers my other half at the moment?"

_"Well, Lex, you say you have clear objectives, but I doubt this, you are not constructing plans to capture the boy."_

"Don't worry, I have that covered."

_"No you do not."_

"And how exactly would you know?"

_"You seem to be forgetting we share thoughts and memories."_

"Maybe this time, I just haven't shared my plans with you."

_"Impossible, we share one mind."_

"Let me remind you that you still maintain to keep secrets from me, no matter how willing I was to hear them."

_"Subconsciously, you do not. Now we will not be successful if we are not one with each other"_

"If it hasn't been blatantly obvious, we are not one. You don't exist, you're a figment of my imagination, a useless one at that. You're nothing more than a distraction, and I don't need you anymore."

_"But without me how will you obtain your memories?"_

"It's simple, I already have them. Ever since you first appeared before me, bits of my memory have been entering my mind, not to mention all the detectives and investigators I have now, digging up the secrets to my past, I remember my life."

_"Do you remember the earthly name of Kal-El?"_

"Admittedly, no."

_"Then it seems we are both at a dead end."_

"You don't seem to understand, the identity of Superman is not a priority of mine, at least not at the moment. Superman is just an obstacle in a bigger scheme."

_"What scheme?"_

Lex smirked.

"You don't need to know."

* * *

Conner sped into Metropolis and toward his objective. He entered a skyscraper and raced to the penthouse apartment. The room was dark and empty. Emil Hamilton was waiting for him out front with a cup of coffee and an impatient look on his face, and a headset in his ear.

"Hi." Conner said.

"You wanted to see me?" Emil asked.

"Yeah, but, where am I?"

"Clark never told you? This is the Watchtower, headquarters of the Justice League, Tess and Chloe used to manage this place, but I took over in their absences."

"Wait, you're a member?"

"Yes, after the team went public I decided to become a permanent active member and not just an emergency physician, I took to engineering and began developing more technology for the League to use."

"So can you help me?"

"I'm pretty sure I would be able to. What is the problem?"

"I saw him again, in a dream, Alexander that is."

"Alexander?"

"Yes, and I don't know what to do, I don't think it was just a dream, I think it meant something."

"It may have just been an illusion brought on by your fears of his return."

"Or maybe it's a warning. I wanted to know if you could analyze my DNA, see if the Kryptonian in me is reseeding."

"It would be highly unlikely."

"I just need to know. Can you help me?"

"Of course, but first I'll need to extract some blood."

"How do you plan on doing that?"

"With a Blue Kryptonite medical needle, we had one built just for Clark."

"Okay."

Emil went to his desk and retrieved the needle.

"Now, this will only take a second."

Emil injected the needle into Conner, who twitched as he bled out.

"I should have your results in an hour or so, but now I have work to do." Emil said as he ran toward the computer and pressed his headset.

"Cyborg, you have three on your tail." He yelled.

* * *

Lena walked into the Torch office. The lights were off and it was empty. As she turned on the light, Zoe and Clayton jumped from behind their desk.

"Surprise!" They yelled.

"Guys?" Lena asked.

"Your story made the cover of Smallville Ledger!" Zoe said.

"Yeah, and you've only been here for 2 months." Clayton said. "We've been doing this for 2 years and haven't done anything like that. You should be proud."

"Thanks guys, but I'd rather skip the festivities; I have rather urgent matters to attend to."

"What's wrong?"

"It's nothing really, just another scoop."

"Come on, the story can wait."

"Not really, in fact I need it published by the end of today. Can you guys run it for me?"

"What's the story?"

Lena typed in the headline for the article.

_**Reporter Confesses. Evidence Was Planted.**_

Lena leaned into her chair as Zoe and Clayton looked at her, in disbelief.

"I can explain."

* * *

Clark walked into the house with Martha and held the door open for her.

"You know Clark you don't need to help me inside."

"You need to rest, Ma."

"Well what are you going to do carry me around the house?"

"If I need to."

"Clark this isn't the first time I've been in a hospital, I did get shot at last year."

"Don't remind me."

"By the way where's Conner?"

"Before we left he was building the barn. I'll check out back for him."

Clark sped into the barn and saw Conner on the floor yelling in pain.

"Conner!" Clark yelled as he ran over to him.

Conner's phone was on the ground and Emil's voice was yelling his name. Clark picked up the phone.

"Emil? What's going on?" He asked.

"It's Conner, his human genes are conflicting with his Kryptonian genes, fighting for control of his body. It's happening at a rapid rate his cells are mutating that's why he's feeling so much pain."

"His Luthor side is coming out!"

Conner's dark hair began to fade colors and turned red, as he rolled over on the barn floor. He stopped screaming and stood up, heat vision fluctuating in his eyes.

"Conner, listen to me, we're going to get you help."

"No!" Conner yelled.

He melted his phone with his heat vision and then shot Clark with a blast of heat vision and Clark catapulted into the wall. Conner ran over to him and grabbed him by the neck.

"I am not Conner!" He yelled , and then sped off.

* * *

Lena walked out to Clayton's truck with Zoe and Clayton next to her.

"So that's what happened." She said as she finished explaining.

"Are you really going to give up on such an amazing accomplishment because of one hack's bluff?" Clayton asked.

"But what if it wasn't a bluff?"

"Then call the police."

"Zoe it's your family."

"Look, I'm not going to let you give up over something that ridiculous. Who is this guy anyway?"

"Don't know, but I've never seen him in this school and it's obvious he's not a student."

Clayton started his car and began driving.

"So the retraction, are you really still going to print it?"

"I don't think I have a choice, not a smart one at least."

A black van pulled up behind Clayton's truck and got dangerously close.

"This guy must be in a rush. I'm going to let him pass." Clayton said.

He pulled to the side as the van accelerated and bumped into him.

"What is up with this guy?" Clayton asked.

The driver accelerated again and hit the pickup truck. Clayton's pickup swerved and hit the side of the road, and fell sideways. The SUV stopped next to his truck and the driver jumped out with 2 others. Lena looked out of her window.

"It's him!" She yelled.

The three men drew sub machine guns on the trio.

"Out the car!" The man yelled as he pointed his gun directly at Lena.

Lena didn't move, and instead just stared at the gun in fear.

"I said out the damn car!" The man yelled as he broke the glass of the window.

He unlocked the car and opened the door. He dragged Lena out the car.

"No!" She yelled

"Lena!" Clayton yelled.

The other two men held their guns at Zoe and Clayton.

"We're stuck!" Zoe yelled.

"Don't just stand there! Get rid of 'em. We don't need witnesses." The man yelled.

The two men began firing at the truck, their bullets nearly invisible as they exited their barrels. Time seemed to slow down as Clayton tried wrapping himself around Zoe. And then he closed his eyes. He could hear the bullets as they impacted, but didn't feel the pain. He opened his eyes and looked out the window, he could feel relief hit him like a breeze. The men were knocked out on the floor.

"Superman." He whispered to Zoe.

He saw a red cloth cape, with a yellow S-shield on it.

"Don't move, Superman!" The leader yelled as he pointed his gun at Lena's head.

"Tom Monaghan, also known as the Hitman, Green Arrow told me you were coming to Smallville." Clark began.

"I thought I took him out." Monaghan said "I guess he's better than I thought."

"Yes." Clark said as he ran toward Tom, and grabbed him by the collar. "And he sends his regards."

Clark punched Tom lightly in the abdomen and Tom bounced back a few feet, and fell unconscious. He turned around and lifted the car up and placing it back onto the road. Zoe and Clayton jumped out and ran toward Lena.

"Now, you three should head home." Clark said with a smile. "And please, stay out of trouble"

The three nodded in awe as Clark smiled lightly, grabbed Monaghan and took off flying.

"Haven't we seen him before?" Clayton asked Zoe.

"Of course we have, it's Superman." Zoe replied.

"Not what I meant." Clayton replied.

* * *

Lex walked toward his Private Jet, as his employees packed his cargo.

"Hurry up people, I need to be back in Metropolis tonight!"

"Mr. Luthor, Agent Graham has contacted us."

"What's the news?"

"He said they were close to acquiring the targets, and then they were taken out by a blur, they couldn't tell if it was Superman or not."

"I want you to delete all records of Agent Monaghan from our databases. As of now, he never worked with us."

"Yes sir."

"Same for the Agents, we need them taken out!"

"Mr. Luthor, we're clear for takeoff." The pilot said out of the door.

"It's about time."

Lex stepped inside and took his seat, as the jet rolled out of the hangar and onto the runway. As the plane lifted up, it rocked to its side.

"What the hell?"

It rocked to the left and right and then regained its balance. Lex looked out of his window and onto his wing. Conner had his hands buried deep into the metal wing and was climbing his way to Lex's window. Lex jumped out of his seat in shock. Conner jumped off of the wing and grabbed onto the side of the plane, as the wind below him pushed him in different directions. He buried his fingers into the Metal door and pulled it off of its hinges. The metal door hurtled and crashed onto the land below. Conner jumped inside of the plane and walked through. Security ran toward him with their guns loaded.

"Freeze!" They yelled.

"Don't let him get to Mr. Luthor."

Conner sped through them and knocked them all into the walls of the plane. He punched down the door into Luthor's private cabin. It was empty. He turned around and felt pain as hard metal hit his face. He fell back, with blood on his face. When he looked up he saw a metal gun with a green glowing muzzle facing him.

* * *

Clark lifted his glasses off of his face as he fixed his jacket and walked back into the Kent House.

"I've checked the all of Smallville, Edge City and Metropolis, Conner's gone." Clark said.

"Do you think he left Kansas?" Martha asked.

"Possibly, but I would have noticed him. Not a lot of people super-speed around anymore."

"Where could he be?"

"If there's one thing I know, wherever Conner is, Lex is not far behind. I need to get to Watchtower, I'll be back later."

"Okay."

Clark sped out of the barn.

* * *

"You've returned." Lex said. "It's almost ironic, no matter where I go I always seem to run into you. And now you've changed your hair, I hope you weren't dumb enough to think that was a believable disguise. But you know, I never quite got your name."

"I am...Alexander" Conner paused. "I am Lex Luthor."

"I can assure you, you are sadly mistaken." Lex said, chuckling.

"I am you. You created me yourself."

"I don't remember having any children."

"I'm a clone, my DNA came from you."

"A clone?" Lex said. He had just briefly remembered some of what happened to him before losing his memory, the fragments that the Other Lex helped him remember.

"You are my...genetic father, and I've returned to the Luthor name."

"Your story doesn't add up, you say you're one of mine, yet you have the powers of a god...or a Kryptonian. You even share the vulnerability to Meteor Rock."

"My powers come from Superman, half of his blood is mine as well."

"A hybrid?" Lex said, astonished "Just like…LNA-3."

"There's another? Like me?"

"Yes…and if your powers manifested, hers should have as well."

"I have to find her."

"Do you really believe I would let you do that? For months, I've tried stopping you, now I have you in my clutches. Now, I can gain the one thing people like Superman, and you, have made me lose."

"And what's that?"

"My pride." Lex said as he pointed the gun at Conner. "There's only one Lex Luthor…and that's me!"

Conner stood up, and tackled Lex, and knocked the gun out of his hand. Lex pushed Conner off of him and rolled over to the gun. He stepped back and aimed the gun at Conner and shot a single Kryptonite bullet. The bullet pierced Conner's skin and entered his abdomen.

"What are you doing?" Other Lex said as he appeared, out of thin air. "Don't let your human emotions get in the way of our plan."

"He's a bump on the road, one that I will remove."

"We need the boy, for greater plans."

"Last time I checked this was my mind, and my body. My decisions."

"You will ruin everything!"

Conner looked on in confusion as Lex seemed to yell at the wall.

"This, partnership, has reached a dead-end it seems. You are no longer a suitable vessel for my agenda."

"Vessel?"

Lex was horrified, as he saw his counterparts face distort and shift and his body twist and elongate. He turned into a symbol. Three dots with lines connecting them in the center.

"Who are you?" Lex asked.

"I am the Brain Interactive Construct."

* * *

Pain soured through Lex, as metal nanobots seeped through his mind and crawled out of his nostrils.

"What are you doing?" He yelled.

"Removing myself."

Lex fell as the last few nanobots fell out of him, and like a swarm hovered toward Conner, who had nearly passed out from his wounds.

"No!" He yelled.

He forced out a blast of heat vision, that sent the swarm into a frenzy and melted the metal of the cabin. Lex used the distraction, and ran for the Cargo in the front cabin. The swarm of nanobots saw him move and raced after him. Lex picked up a taser gun from one of his unconscious guard, and the Nanobots stopped at the unconscious bodies of his guard and impaled their foreheads and began extracting their memories. Lex looked back in horror as blood and flesh spilled from their bodies, and the nanobots killed each one of them. He unlocked the door of the Cargo room and ran inside, for the Prometheus prototype. He unlocked the container, as he heard the metal buzz of Brainiac's androids. He couldn't suit up, so instead he shot the taser wire. It hooked onto a few nanobots and electrocuted them and several others. The swarm exploded in sparks and fell, and he watched, helpless, as some of them still flew toward him, and then turned away from him, and aimed for the Prometheus armor. They crawled inside of the armor, and hid from Lex.

"What are you doing?" He asked as he backed away.

The suit activated, and the nanobots combined to form a metallic head.

"Assimilation complete, modification of suit hardware complete."

"What have you done?"

"Re-made myself in my own image, I no longer require human disguises, Kal-El has revealed himself, and in order to defeat him, I must do the same. It is inevitable."

Brainiac grabbed Lex by the neck.

"Your services may still be required. I will keep you as a failsafe."

He blasted an energy beam and created a hole in the side of the plane and the metal slowly peeled off as the wind hit it. And slowly, the wing ignited in flame and fell off. Brainiac leaped out of the plane, and took off flying.

* * *

Conner felt light-headed as the Plane fell faster and faster. He struggled to stay awake.

"I'm not going to make it." He whispered.

As he realized his fate, he slowly closed his eyes.


End file.
